[BioC] GO term enrichment

[Martin Morgan]

On 02/25/2011 07:38 AM, Ludwig Eichinger wrote:
> Dear colleagues,
> 
> we would like to analyse gene ontology term enrichment for a RNAseq
> experiment of human cells. Can we do this with bioconductor (which R
> version do we need) and if yes, how can we do it?

Hi Ludwig --

The goseq package available with R-2.12.* is one example. It has an
extensive vignette and publication(s).

  ## next two lines once only, to install goseq & dependencies
  source('http://bioconductor.org/biocLite.R')
  biocLite('goseq')
  browseVignette('goseq')
  citation('goseq')

Martin
> 
> Thank you very much for your advice.
> 
> Best regards
> 
> Ludwig Eichinger
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Prof. Dr. Ludwig Eichinger
> Centre for Biochemistry
> Medical Faculty
> University of Cologne
> Joseph-Stelzmann-Str. 52
> D-50931 Koeln
> 
> Tel. 0049-221-4786928
> FAX  0049-221-4786979
> 
> Dictyostelium Genome Project and Fuctional Analysis:
> http://www.uni-koeln.de/med-fak/biochemie/transcriptomics/
> http://www.uni-koeln.de/dictyostelium/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
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